Polygenic Score (PGS) ID: PGS002027

Predicted Trait
Reported Trait Diabetic retinopathy
Mapped Trait(s) diabetic retinopathy (EFO_0003770)
Additional Trait Information endocrine/metabolic
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_250.7
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 389,029
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
391,124 individuals European UK (+ Ireland) UKB

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM011090 PSS009289|
European Ancestry|
19,330 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Diabetic retinopathy Partial Correlation (partial-r): 0.0451 [0.031, 0.0592] sex, age, birth date, deprivation index, 16 PCs
PPM011091 PSS009063|
European Ancestry|
4,032 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Diabetic retinopathy Partial Correlation (partial-r): 0.0607 [0.0298, 0.0915] sex, age, birth date, deprivation index, 16 PCs
PPM011092 PSS008617|
European Ancestry|
6,465 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Diabetic retinopathy Partial Correlation (partial-r): 0.0241 sex, age, birth date, deprivation index, 16 PCs
PPM011093 PSS008393|
Greater Middle Eastern Ancestry|
1,162 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Diabetic retinopathy Partial Correlation (partial-r): -0.0311 [-0.0889, 0.027] sex, age, birth date, deprivation index, 16 PCs
PPM011094 PSS008171|
South Asian Ancestry|
6,081 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Diabetic retinopathy Partial Correlation (partial-r): 0.0351 [0.01, 0.0603] sex, age, birth date, deprivation index, 16 PCs
PPM011095 PSS007958|
East Asian Ancestry|
1,764 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Diabetic retinopathy Partial Correlation (partial-r): -0.0302 [-0.077, 0.0168] sex, age, birth date, deprivation index, 16 PCs
PPM011096 PSS007739|
African Ancestry|
2,385 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Diabetic retinopathy Partial Correlation (partial-r): -0.0204 [-0.0606, 0.0199] sex, age, birth date, deprivation index, 16 PCs
PPM011097 PSS008842|
African Ancestry|
3,732 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Diabetic retinopathy Partial Correlation (partial-r): 0.0062 [-0.0259, 0.0384] sex, age, birth date, deprivation index, 16 PCs

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS009063 4,032 individuals European Poland (NE Europe) UKB
PSS008617 6,465 individuals European Italy (South Europe) UKB
PSS008393 1,162 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009289 19,330 individuals European UK (+ Ireland) UKB
PSS008171 6,081 individuals South Asian India (South Asia) UKB
PSS008842 3,732 individuals African unspecified Nigeria (West Africa) UKB
PSS007958 1,764 individuals East Asian China (East Asia) UKB
PSS007739 2,385 individuals African American or Afro-Caribbean Carribean UKB